Abstract 2941: SureSelect Cancer CGP assay for detection of the common mutation types found in cancer
Authors: Akanksha Khare, Anne Bergstrom Lucas, Joachim de-Schrijver, Manjula Aliminati, Hanjun Shin, Linus Forsmark, Barbara Novak, Jeroen Crappe, Michael Ruvolo
Journal: Cancer Research (2022)

Abstract Background: The current standard for genomic profiling of cancer tissues relies upon multiple technologies to aid in tumor characterization. Here we describe a comprehensive genomic profiling pan-cancer assay that detects single nucleotide polymorphisms and small insertions/deletions, somatic copy number alterations, translocations, RNA fusions and exon-skipping events, as well as determining Tumor Mutation Burden (TMB) score and Microsatellite Instability (MSI) using both Tumor-only and Tumor-Normal analysis methods. The assay consists of hybrid capture-based panels for enrichment of both gDNA and total RNA extracted from FFPE samples. DNA and RNA samples are processed using Agilent’s SureSelect XT HS2 chemistry, including full automation on the Magnis NGS prep system, and analyzed using the Alissa Reporter software, streamlining the workflow and analysis. Methods: Content of the assay was curated using literature review and input from multiple cancer databases. The assay employs a modular design with a DNA capture panel covering all actionable genes/variants as well as genes that are commonly mutated across cancer types, and an RNA panel covering fusion driver mutations. Probes were designed to cover the exons of all genes with enhanced coverage of clinically actionable mutations. Selected genes in the DNA panel have additional coverage allowing for copy number determination and detection of translocations in hot-spot regions. The data analysis pipeline in the Alissa Reporter software allows for the seamless analysis of the sequencing results and provides sensitive and accurate detection of the variants. The software also allows for visualization in the genomic context, QC metrics tracking, and results reporting functionalities, giving users a full picture of their samples. Results: Performance was demonstrated on &amp;gt;80 FFPE samples and reference standards with accuracy determined by concordance with gold-standard measurements. For TMB analysis, FFPE samples were analyzed using the SureSelect Cancer CGP assay and whole-exome sequencing. The values from both assays show high correlation (r &amp;gt; 0.8). Microsatellite instability measured by the assay was 93% concordant with MSI-PCR. ERBB2 copy number determination in breast cancer samples was 87% concordant with FISH, while translocation and RNA fusion detection were both &amp;gt;85% concordant to FISH for a set of ALK+ NSCLC samples. Conclusion: This work represents an important advancement in the development of an assay to detect the common mutation types found in cancer as well as provide information on the genomic biomarkers, TMB and MSI from a single FFPE sample. For Research use Only Citation Format: Akanksha Khare, Anne Bergstrom Lucas, Joachim de-Schrijver, Manjula Aliminati, Hanjun Shin, Linus Forsmark, Barbara Novak, Jeroen Crappe, Michael Ruvolo. SureSelect Cancer CGP assay for detection of the common mutation types found in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2941.